checkpoint for the changes on yml

src/sirocco/core/_tasks/shell_task.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from dataclasses import dataclass
+from dataclasses import field, dataclass
 from typing import ClassVar
 
 from sirocco.core.graph_items import Task
@@ -12,5 +12,5 @@ class ShellTask(Task):
 
     command: str | None = None
     command_option: str | None = None
-    input_arg_options: dict[str, str] | None = None
+    input_arg_options: dict[str, str] = field(default_factory=dict) 
     src: str | None = None

src/sirocco/core/graph_items.py

@@ -2,6 +2,8 @@
 
 from dataclasses import dataclass, field
 from itertools import chain, product
+from os.path import expandvars
+from pathlib import Path
 from typing import TYPE_CHECKING, Any, ClassVar, Self
 
 if TYPE_CHECKING:
@@ -116,6 +118,11 @@ def from_config(cls, config: DataBaseModel, coordinates: dict) -> Self:
             coordinates=coordinates,
         )
 
+    @property
+    def path(self) -> Path:
+        # TODO yaml level?
+        return Path(expandvars(self.src))
+
 
 @dataclass(kw_only=True)
 class Cycle(GraphItem):

src/sirocco/parsing/_yaml_data_models.py

@@ -29,18 +29,30 @@ class _NamedBaseModel(BaseModel):
     name: str
 
     def __init__(self, /, **data):
+        super().__init__(**self.merge_name_and_specs(data))
+
+    @staticmethod
+    def merge_name_and_specs(data: dict) -> dict:
+        """
+        Converts dict of form
+
+        `{my_name: {'spec_0': ..., ..., 'spec_n': ...}`
+
+        to
+
+        `{'name': my_name, 'spec_0': ..., ..., 'spec_n': ...}`
+
+        by copy.
+        """
         name_and_spec = {}
-        # - my_name:
-        #     ...
         if len(data) != 1:
             msg = f"Expected dict with one element of the form {{'name': specification}} but got {data}."
             raise ValueError(msg)
         name_and_spec["name"] = next(iter(data.keys()))
         # if no specification specified e.g. "- my_name:"
         if (spec := next(iter(data.values()))) is not None:
             name_and_spec.update(spec)
-
-        super().__init__(**name_and_spec)
+        return name_and_spec
 
 
 class _WhenBaseModel(BaseModel):
@@ -228,14 +240,11 @@ def check_period_is_not_negative_or_zero(self) -> ConfigCycle:
             raise ValueError(msg)
         return self
 
+from typing import Literal
 
-class ConfigTask(_NamedBaseModel):
-    """
-    To create an instance of a task defined in a workflow file
-    """
-
+class ConfigTaskBase(_NamedBaseModel):
     # config for genric task, no plugin specifics
-    parameters: list[str] = []
+    parameters: list[str] = Field(default_factory=list)
     host: str | None = None
     account: str | None = None
     plugin: str | None = None
@@ -256,7 +265,17 @@ def convert_to_struct_time(cls, value: str | None) -> time.struct_time | None:
         return None if value is None else time.strptime(value, "%H:%M:%S")
 
 
-# TODO(maybe): ConfigTaskIcon(ConfigTask) and ConfigTaskShell(ConfigTask)
+
+class ConfigTaskShell(ConfigTaskBase):
+    plugin: Literal["shell"]
+    command: str 
+    command_option: str = ""
+    input_arg_options: dict[str, str] = Field(default_factory=dict) 
+    src: str | None = None
+
+
+class ConfigTaskIcon(ConfigTaskBase):
+    plugin: Literal["icon"]
 
 
 class DataBaseModel(_NamedBaseModel):
@@ -297,11 +316,20 @@ class ConfigData(BaseModel):
     available: list[ConfigAvailableData] = []
     generated: list[ConfigGeneratedData] = []
 
+from typing import Annotated
+from pydantic import Discriminator, Tag
+
+def get_plugin_from_named_base_model(data: dict) -> str:
+    plugin =_NamedBaseModel.merge_name_and_specs(data).get("plugin", "")
+    return plugin
 
 class ConfigWorkflow(BaseModel):
     name: str | None = None
     cycles: list[ConfigCycle]
-    tasks: list[ConfigTask]
+    tasks: list[Annotated[
+        Annotated[ConfigTaskIcon, Tag("icon")] |
+        Annotated[ConfigTaskShell, Tag("shell")],
+        Discriminator(get_plugin_from_named_base_model)]]
     data: ConfigData
     parameters: dict[str, list] = {}
     data_dict: dict = {}

src/sirocco/workgraph.py

@@ -79,7 +79,7 @@ def __init__(self, core_workflow: core.Workflow):
 
     def _validate_workflow(self):
         """Checks if the defined workflow is correctly referencing key names."""
-        for cycle in self._core_workflow.cycles.values():
+        for cycle in self._core_workflow.cycles:
             try:
                 aiida.common.validate_link_label(cycle.name)
             except ValueError as exception:
@@ -109,7 +109,7 @@ def _add_aiida_initial_data_nodes(self):
         """
         Nodes that correspond to data that are available on initialization of the workflow
         """
-        for cycle in self._core_workflow.cycles.values():
+        for cycle in self._core_workflow.cycles:
             for task in cycle.tasks:
                 for input_ in task.inputs:
                     if input_.available:
@@ -126,7 +126,7 @@ def parse_to_aiida_label(label: str) -> str:
     def get_aiida_label_from_unrolled_data(obj: core.BaseNode) -> str:
         """ """
         return AiidaWorkGraph.parse_to_aiida_label(
-            f"{obj.name}" + "_".join(f"_{key}_{value}" for key, value in obj.parameters.items())
+            f"{obj.name}" + "_".join(f"_{key}_{value}" for key, value in obj.coordinates.items())
         )
 
     @staticmethod
@@ -137,7 +137,7 @@ def get_aiida_label_from_unrolled_task(obj: core.BaseNode) -> str:
         #      Otherwise the label is not unique
         # --> task name + date + parameters
         return AiidaWorkGraph.parse_to_aiida_label(
-            f"{obj.name}" + "_".join(f"_{key}_{value}" for key, value in obj.parameters.items())
+            f"{obj.name}" + "_".join(f"_{key}_{value}" for key, value in obj.coordinates.items())
         )
 
     def _add_aiida_input_data_node(self, input_: core.UnrolledData):
@@ -156,17 +156,19 @@ def _add_aiida_input_data_node(self, input_: core.UnrolledData):
             raise ValueError(msg)
 
     def _add_aiida_task_nodes(self):
-        for cycle in self._core_workflow.cycles.values():
+        for cycle in self._core_workflow.cycles:
             for task in cycle.tasks:
                 self._add_aiida_task_node(task)
         # after creation we can link the wait_on tasks
         # TODO check where this is now
-        #for cycle in self._core_workflow.cycles.values():
+        #for cycle in self._core_workflow.cycles:
         #    for task in cycle.tasks:
         #        self._link_wait_on_to_task(task)
 
     def _add_aiida_task_node(self, task: core.UnrolledTask):
         label = AiidaWorkGraph.get_aiida_label_from_unrolled_task(task)
+        if task.command is None:
+            raise ValueError(f"The command is None of task {task}.")
         workgraph_task = self._workgraph.tasks.new(
             "ShellJob",
             name=label,
@@ -189,7 +191,7 @@ def _link_wait_on_to_task(self, task: core.UnrolledTask):
         workgraph_task.wait = wait_on_tasks
 
     def _add_aiida_links(self):
-        for cycle in self._core_workflow.cycles.values():
+        for cycle in self._core_workflow.cycles:
             self._add_aiida_links_from_cycle(cycle)
 
     def _add_aiida_links_from_cycle(self, cycle: core.UnrolledCycle):

tests/files/configs/test_config_parameters.yml

@@ -91,5 +91,5 @@ data:
         src: yearly_analysis
 
 parameters:
-  foo: [0, 1]
-  bar: {arange: [3, 4]}
+  foo: [0, 1, 2]
+  bar: [3.0, 3.5]